One-way or two-way factor model for matrix sequences?

This paper investigates the issue of determining the dimensions of row and column factor spaces in matrix-valued data. Exploiting the eigen-gap in the spectrum of sample second moment matrices of the data, we propose a family of randomised tests to check whether a one-way or two-way factor structure exists or not. Our tests do not require any arbitrary thresholding on the eigenvalues, and can be applied with (virtually) no restrictions on the relative rate of divergence of the cross-sections to the sample sizes as they pass to infinity. Although tests are based on a randomisation which does not vanish asymptotically, we propose a de-randomised, “strong” (based on the Law of the Iterated Logarithm) decision rule to choose in favour or against the presence of common factors. We use the proposed tests and decision rule in two ways. We further cast our individual tests in a sequential procedure whose output is an estimate of the number of common factors. Our tests are built on two variants of the sample second moment matrix of the data: one based on a row (or column) “flattened” version of the matrix-valued sequence, and one based on a projection-based method. Our simulations show that both procedures work well in large samples and, in small samples, the one based on the projection method delivers a superior performance compared to existing methods in virtually all cases considered.</p

Periodicity of Monoisotopic Mass Isomers and Isobars in Proteomics

We report trends in the theoretically derived number of compositionally distinct peptides (i.e., peptides made up of different amino acid residues) up to a nominal mass of 1000. A total of 21 amino acid residues commonly found in proteomics studies are included in this study, 19 natural, nonisomeric amino acid residues as well as oxidated methione and acetamidated cysteine. The number of possibilities is found to increase in an exponential fashion with increasing nominal mass, and the data show a periodic oscillation that starts at mass ∼200 and continues throughout to 1000. Note that similar effects are reported in the companion article on fragment ions from electron capture/transfer dissociation (ECD/ETD) (Mao et al. Anal. Chem. 2011, DOI: 10.1021/ac201619t). The spacing of this oscillation is ∼15 mass units at lower masses and ∼14 mass units at higher nominal masses. This correlates with the most common mass differences between the amino acid building blocks. In other words, some mass differences are more common than others, thus determining the periodicity in this data. From an analytical point of view, nominal masses with a larger number of compositionally distinct peptides include a substantial number of isomers, which cannot be separated based on mass. Consequently, even ultrahigh mass accuracy (i.e., 0.5 ppm) does not lead to a substantially enhanced rate of identification. Conversely, for adjacent nominal masses with a lower number of isomers, moderately accurate mass (i.e., 10 ppm) gives a higher degree of certainty in identification. These effects are limited to the mass range between 200 and 500 Da. At higher masses, the percentage of uniquely identified peptides drops off to close to zero, independent of nominal mass, due the inherently high number of isomers. While the exact number of isobars/isomers at each nominal mass depends on the amino acid building blocks that are considered, the periodicity in the data is found to be remarkably robust; for instance, inclusion of phosphorylated residues barely affects the pattern at lower masses (i.e., <500 Da)

Online Change-point Detection for Matrix-valued Time Series with Latent Two-way Factor Structure

This paper proposes a novel methodology for the online detectionof changepoints in the factor structure of large matrix time series. Ourapproach is based on the well-known fact that, in the presence of achangepoint, the number of spiked eigenvalues in the second momentmatrix of the data increases (e.g., in the presence of a change in theloadings, or if a new factor emerges). Based on this, we propose twofamilies of procedures - one based on the fluctuations of partial sums,and one based on extreme value theory - to monitor whether the firstnon-spiked eigenvalue diverges after a point in time in the monitoringhorizon, thereby indicating the presence of a changepoint. Our proce-dure is based only on rates; at each point in time, we randomise theestimated eigenvalue, thus obtaining a normally distributed sequencewhich isi.i.d.with mean zero under the null of no break, whereasit diverges to positive infinity in the presence of a changepoint. Webase our monitoring procedures on such sequence. Extensive simula-tion studies and empirical analysis justify the theory. An R packageimplementing the procedure is available on CRAN.</p

Frictional Effect of Helical Pile Installation in Uniform Clays

The application of helical piles offshore has been attractive due to its 'quiet' installation and retrieving potential, which makes it more environmentally friendly and economical. In this paper, single large plate helical piles in uniform clays are studied for offshore applications. The torsional installation of the helical piles is simulated using three-dimensional large deformation finite element (LDFE) analysis with Coupled Eulerian Largrangian (CEL) method in ABAQUS. The effects of interface friction between the helical pile and the clay are studied on the required torque and crowd force during torsional installations. It is found that the friction coefficient has minimal influence on the installation crowd force but has a greater influence on the installation torque required. The increased installation torque due to frictional effect can be formulated as a linear function of the friction coefficient at a given normalized penetration depth. The soil flow mechanism around the helical plate is revealed to explain the frictional effects. To provide more insight, complementary small strain analysis is conducted studying helix end effects modelled as a strip footing. The effects of plate embedment depth (H) and the soil undrained shear strength (su) on helical pile installation responses are also studied. In flat plate end bearing capacity study, the horizontal plate end bearing factor (Nc) is similar to that of vertical plate end bearing factor with embedment ratio of H/t =20

One-way or two-way factor model for matrix sequences?

This paper investigates the issue of determining the dimensions of row and column factor spaces in matrix-valued data. Exploiting the eigen-gap in the spectrum of sample second moment matrices of the data, we propose a family of randomised tests to check whether a one-way or two-way factor structure exists or not. Our tests do not require any arbitrary thresholding on the eigenvalues, and can be applied with (virtually) no restrictions on the relative rate of divergence of the cross-sections to the sample sizes as they pass to infinity. Although tests are based on a randomisation which does not vanish asymptotically, we propose a de-randomised, “strong” (based on the Law of the Iterated Logarithm) decision rule to choose in favour or against the presence of common factors. We use the proposed tests and decision rule in two ways. We further cast our individual tests in a sequential procedure whose output is an estimate of the number of common factors. Our tests are built on two variants of the sample second moment matrix of the data: one based on a row (or column) “flattened” version of the matrix-valued sequence, and one based on a projection-based method. Our simulations show that both procedures work well in large samples and, in small samples, the one based on the projection method delivers a superior performance compared to existing methods in virtually all cases considered.</p

SEDyConv: Spatially enhanced multi-dimensional dynamic convolution for medical multi-organ segmentation in CTs

Automated multi-organ segmentation presents a considerable challenge owing to the diversity of organs and individual variations. Current state-of-the-art deep-learning techniques rely primarily on static kernel weights that are fixed after training, thereby limiting their flexibility in adapting to diverse inputs. In this study, we propose a novel multi-organ segmentation method using a plug-and-play three-dimensional dynamic convolution module. This method is designed to address the challenges posed by the variability of CT scans in contrast to static segmentation models. We uniquely leverage multiple input-dependent attention mechanisms to adjust the coefficients across four dimensions of convolutional kernels dynamically, offering enhanced adaptability. This approach surpasses traditional feature-based dynamic methods in terms of flexibility, which is attributable to the global sharing of kernel parameters and a smaller kernel shape. In addition, we utilize a refined local block to preserve the spatial properties and extend the convolutional kernel space to N dimensions, thereby efficiently enhancing the representational capabilities of the model through higher-dimensional feature fusion. Furthermore, we design dynamic switches to integrate multi-dimensional global and local information adaptively, guiding the model to generate feature maps that closely align with the input characteristics. Visualizations of the dynamic coefficients and features generated by different inputs clearly demonstrate the adaptability of our method. Extensive experiments on four multi-organ segmentation datasets with various labeled organs and scales indicate that our proposed method outperforms other state-of-the-art methods in terms of improving the segmentation accuracy, particularly for organs with complex morphologies or small sizes. Code available at: https://github.com/lihaoqin168/SEDyConv.</p

UNC50 Prompts G1/S Transition and Proliferation in HCC by Regulation of Epidermal Growth Factor Receptor Trafficking

<div><p>Background</p><p>UNC50 has long been recognized as a Golgi apparatus protein in yeast, and is involved in nicotinic receptor trafficking in <i>Caenorhabditis elegans</i>, but little is known about <i>UNC50</i> gene function in human biology despite it being conserved from yeast to high eukaryotes.</p><p>Objectives</p><p>We investigated the relation between UNC50 and human hepatocellular carcinoma (HCC) and the potential mechanisms underlying HCC development.</p><p>Methods</p><p><i>UNC50</i> mRNA expression patterns in 12 HCC and adjacent non-cancerous tissues determined using northern blotting were confirmed by real-time PCR in another 44 paired tissues. Microarray experiments were used to screen for global effects of UNC50 knockdown in the Hep3B cell line, and were confirmed by real-time PCR, western blotting, flow cytometry, and tetrazolium assay in both UNC50 overexpression and knockdown Hep3B cells.</p><p>Results</p><p>UNC50 expression levels were upregulated in HCC tissues in comparison with the adjacent non-cancerous tissues. UNC50 knockdown reduced mRNA levels of the downstream targets of the epidermal growth factor receptor (EGFR) pathway: cyclin D1 (<i>CCND1</i>), <i>EGF</i>, matrix metalloproteinase-7 (<i>MMP7</i>), aldose reductase-like 1 (<i>AKR1B10</i>), cell surface–associated mucin 1 (<i>MUC1</i>), and gastrin (<i>GAST</i>). Moreover, UNC50 influenced EGF, inducing cell cycle entry by affecting cell surface EGFR amounts.</p><p>Conclusions</p><p><i>UNC50</i> may plays some roles in HCC progression by affecting the EGFR pathway.</p></div

Frictional Effect of Helical Pile Installation in Uniform Clays

The application of helical piles offshore has been attractive due to its 'quiet' installation and retrieving potential, which makes it more environmentally friendly and economical. In this paper, single large plate helical piles in uniform clays are studied for offshore applications. The torsional installation of the helical piles is simulated using three-dimensional large deformation finite element (LDFE) analysis with Coupled Eulerian Largrangian (CEL) method in ABAQUS. The effects of interface friction between the helical pile and the clay are studied on the required torque and crowd force during torsional installations. It is found that the friction coefficient has minimal influence on the installation crowd force but has a greater influence on the installation torque required. The increased installation torque due to frictional effect can be formulated as a linear function of the friction coefficient at a given normalized penetration depth. The soil flow mechanism around the helical plate is revealed to explain the frictional effects. To provide more insight, complementary small strain analysis is conducted studying helix end effects modelled as a strip footing. The effects of plate embedment depth (H) and the soil undrained shear strength (su) on helical pile installation responses are also studied. In flat plate end bearing capacity study, the horizontal plate end bearing factor (Nc) is similar to that of vertical plate end bearing factor with embedment ratio of H/t =20

Imaged normal atrial activation from subject NS7.

IVC = Inferior vena cava; LA = left atrium; LAA = Left atrial appendage; RA = right atrium; SVC = Superior vena cava.</p

Results with recording sites covering a full chamber.

<p><b>First column:</b> Imaged activation time maps. <b>Second column:</b> Endocardial surface of 3D ARI maps. <b>Third column:</b> Three cross section views of 3D ARI maps. <b>Fourth column:</b> Interpolated CARTO ARI maps. Yellow stars in the ARI maps represent the longest ARI sites. All the maps were color-coded from red to blue. 3D = 3-dimensional; ARI = activation recovery interval; CC = correlation coefficient; LE = localization error; LV = left ventricle; RV = right ventricle.</p